Energy Parameters and Novel Algorithms for an Extended Nearest Neighbor Energy Model of RNA
نویسندگان
چکیده
We describe the first algorithm and software, RNAenn, to compute the partition function and minimum free energy secondary structure for RNA with respect to an extended nearest neighbor energy model. Our next-nearest-neighbor triplet energy model appears to lead to somewhat more cooperative folding than does the nearest neighbor energy model, as judged by melting curves computed with RNAenn and with two popular software implementations for the nearest-neighbor energy model. A web server is available at http://bioinformatics.bc.edu/clotelab/RNAenn/.
منابع مشابه
An Improved K-Nearest Neighbor with Crow Search Algorithm for Feature Selection in Text Documents Classification
The Internet provides easy access to a kind of library resources. However, classification of documents from a large amount of data is still an issue and demands time and energy to find certain documents. Classification of similar documents in specific classes of data can reduce the time for searching the required data, particularly text documents. This is further facilitated by using Artificial...
متن کاملAn Improved K-Nearest Neighbor with Crow Search Algorithm for Feature Selection in Text Documents Classification
The Internet provides easy access to a kind of library resources. However, classification of documents from a large amount of data is still an issue and demands time and energy to find certain documents. Classification of similar documents in specific classes of data can reduce the time for searching the required data, particularly text documents. This is further facilitated by using Artificial...
متن کاملSoftware Cost Estimation by a New Hybrid Model of Particle Swarm Optimization and K-Nearest Neighbor Algorithms
A successful software should be finalized with determined and predetermined cost and time. Software is a production which its approximate cost is expert workforce and professionals. The most important and approximate software cost estimation (SCE) is related to the trained workforce. Creative nature of software projects and its abstract nature make extremely cost and time of projects difficult ...
متن کاملAn Algorithm for Predicting Recurrence of Breast Cancer Using Genetic Algorithm and Nearest Neighbor Algorithm
Introduction: Breast cancer is one of the most common types of cancer and the most common type of malignancy in women, which has been growing in recent years. Patients with this disease have a chance of recurrence. Many factors reduce or increase this probability. Data mining is one of the methods used to detect or anticipate cancers, and one of its most common uses is to predict the recurrence...
متن کاملA range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more.
The standard approach for single-sequence RNA secondary structure prediction uses a nearest-neighbor thermodynamic model with several thousand experimentally determined energy parameters. An attractive alternative is to use statistical approaches with parameters estimated from growing databases of structural RNAs. Good results have been reported for discriminative statistical methods using comp...
متن کامل